Fix some documentation regarding corona, bio, wastewater #1286
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asl
reviewed
Apr 30, 2024
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| Note that normal biosyntheticSPAdes mode (via `--bio` option) is a bit different from HMM-guided mode: besides using the special set of profile HMMS representing a family of NRSP/PKS domains also includes a set of assembly graph simplification and processing settings aimed for fuller recovery of biosynthetic gene clusters. | ||
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| ## coronaSPAdes mode | ||
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| Given an increased interest in coronavirus research we developed a coronavirus assembly mode for SPAdes assembler (also known as coronaSPAdes). It allows to assemble full-length coronaviridae genomes from the transcriptomic and metatranscriptomic data. Algorithmically, coronaSPAdes is an rnaviralSPAdes that uses the set of HMMs from [Pfam SARS-CoV-2 2.0](ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam_SARS-CoV-2_2.0/) set as well as additional HMMs as outlined by [(Phan et al, 2019)](https://doi.org/10.1093/ve/vey035). coronaSPAdes could be run via a dedicated `coronaspades.py` script. See [coronaSPAdes preprint](https://www.biorxiv.org/content/10.1101/2020.07.28.224584v1) for more information about rnaviralSPAdes, coronaSPAdes and HMM-guided mode. Output for any HMM-related mode (`--bio`, `--corona`, or `--custom-hmms` flags) is the same with biosyntheticSPAdes' output. | ||
| Given an increased interest in coronavirus research we developed a coronavirus assembly mode for SPAdes assembler (also known as coronaSPAdes). | ||
| It allows to assemble full-length coronaviridae genomes from the transcriptomic and metatranscriptomic data. Algorithmically, coronaSPAdes is an rnaviralSPAdes that uses the set of HMMs from [Pfam SARS-CoV-2 2.0](ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam_SARS-CoV-2_2.0/) set as well as additional HMMs as outlined by [(Phan et al, 2019)](https://doi.org/10.1093/ve/vey035). coronaSPAdes could be run via a dedicated `coronaspades.py` script. See [coronaSPAdes paper](https://academic.oup.com/bioinformatics/article/38/1/1/6354349) for more information about rnaviralSPAdes, coronaSPAdes and HMM-guided mode. Output for any HMM-related mode (`--bio`, `--corona`, or `--custom-hmms` flags) is the same with biosyntheticSPAdes' output. |
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Can we refer to noro paper also as an example to use?
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